Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

Making the impact on research and society : a case study: crowdsourcing solutions developed for the linguistic research and citizen science

Can crowdsourcing solutions serve many masters? Can they be beneficial for both, for the layman or native speakers of minority languages on the one hand and serious linguistic research on the other? How did an infrastructure that was designed to support linguistics turn out to be a solution for raising awareness of native languages? Since 2012 the National Library of Finland has been developing the Digitisation Project for Kindred Languages, in which the key objective is to support a culture of openness and interaction in linguistic research, but also to promote crowdsourcing as a tool for participation of the language community in research. In the course of the project, over 1,200 monographs and nearly 111,000 pages of newspapers in Finno-Ugric languages will be digitised and made available in the Fenno-Ugrica digital collection. This material was published in the Soviet Union in the 1920s and 1930s, and users have had only sporadic access to the material. The publication of open-access and searchable materials from this period is a goldmine for researchers. Historians, social scientists and laymen with an interest in specific local publications can now find text materials pertinent to their studies. The linguistically-oriented population can also find writings to delight them: (1) lexical items specific to a given publication, and (2) orthographically-documented specifics of phonetics. In addition to the open access collection, we developed an open source code OCR editor that enables the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary since these rare and peripheral prints often include already archaic characters, which are neglected by modern OCR software developers but belong to the historical context of kindred languages, and are thus an essential part of the linguistic heritage. When modelling the OCR editor, it was essential to consider both the needs of researchers and the capabilities of lay citizens, and to have them participate in the planning and execution of the project from the very beginning. By implementing the feedback iteratively from both groups, it was possible to transform the requested changes as tools for research that not only supported the work of linguistics but also encouraged the citizen scientists to face the challenge and work with the crowdsourcing tools for the benefit of research. This presentation will not only deal with the technical aspects, developments and achievements of the infrastructure but will highlight the way in which user groups, researchers and lay citizens were engaged in a process as an active and communicative group of users and how their contributions were made to mutual benefit.

Sustaining your Open Source project through training: a Hydra case study

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Hacking User Experience in a Repository Service: ScholarSphere as a Case Study

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

From library repository to university-wide service: Stanford Digital Repository as a case study

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Case study in responsive (re)design

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Developing sustainable value proposition: A case study from manufacturing industry

Increasing pressures to reduce costs, inprove productivity, and lower the environmental impact are forcing suppliers to present evidences of the monetary and societal value they create for the customers and society around. The extant academic literature on the practical activities related to topic is still sparse and this study addresses the gap by developing sustainable customer value proposition for Valmet’s recycled fibre line solution for the Chinese market. The research is based on literature review and single case study method. Theoretically the study is connected to the emerging literature of customer value and life cycle engineering, and to the research of sustainable development in the field of marketing. For exloiting empirical evidences, in-depth supplier interviews and customer survey were conducted. The results suggest that selling of recycled fibre line solution requires tangible and credible evidence of the value and utility which is delivered for the customer. In addition to the economic benefits also societal benefits should be included in the value proposition that are the focus of attention in China. Still, the role of discovered benefits may be contradictory until they are communicated to appropriate decision makers. Managerially the study contributes to the customer value management and quantification knowledge and practices in Valmet’s organization.

Carrier selection and management : A case study on Neste Oil Retail

Service provider selection has been said to be a critical factor in the formation of supply chains. Through successful selection companies can attain competitive advantage, cost savings and more flexible operations. Service provider management is the next crucial step in outsourcing process after the selection has been made. Without proper management companies cannot be sure about the level of service they have bought and they may suffer from service provider's opportunistic behavior. In worst case scenario the buyer company may end up in locked-in situation in which it is totally dependent of the service provider. This thesis studies how the case company conducts its carrier selection process along with the criteria related to it. A model for the final selection is also provided. In addition, case company's carrier management procedures are reflected against recommendations from previous researches. The research was conducted as a qualitative case study on the principal company, Neste Oil Retail. A literature review was made on outsourcing, service provider selection and service provider management. On the basis of the literature review, this thesis ended up recommending Analytic hierarchy process as the preferred model for the carrier selection. Furthermore, Agency theory was seen to be a functional framework for carrier management in this study. Empirical part of this thesis was conducted in the case company by interviewing the key persons in the selection process, making observations and going through documentations related to the subject. According to the results from the study, both carrier selection process as well as carrier management were closely in line with suggestions from literature review. Analytic hierarchy process results revealed that the case company considers service quality as the most important criteria with financial situation and price of service following behind with almost identical weights with each other. Equipment and personnel was seen as the least important selection criterion. Regarding carrier management, the study resulted in the conclusion that the company should consider engaging more in carrier development and working towards beneficial and effective relationships. Otherwise, no major changes were recommended for the case company processes.

Interfirm Information System for Supply Chain Management from the Cloud: An Exploratory Case Study from the Telecom Industry

This study examines the practice of supply chain management problems and the perceived demand information distortion’s (the bullwhip effect) reduction with the interfirm information system, which is delivered as a cloud service to a company operating in the telecommunications industry. The purpose is to shed light in practice that do the interfirm information system have impact on the performance of the supply chain and in particularly the reduction of bullwhip effect. In addition, a holistic case study of the global telecommunications company's supply chain is presented and also the challenges it’s facing, and this study also proposes some measures to improve the situation. The theoretical part consists of the supply chain and its management, as well as increasing the efficiency and introducing the theories and related previous research. In addition, study presents performance metrics for the bullwhip effect detection and tracking. The theoretical part ends in presenting cloud -based business intelligence theoretical framework used in the background of this study. The research strategy is a qualitative case study, supported by quantitative data, which is collected from a telecommunication sector company's databases. Qualitative data were gathered mainly with two open interviews and the e-mail exchange during the development project. In addition, other materials from the company were collected during the project and the company's web site information was also used as the source. The data was collected to a specific case study database in order to increase reliability. The results show that the bullwhip effect can be reduced with the interfirm information system and with the use of CPFR and S&OP models and in particularly combining them to an integrated business planning. According to this study the interfirm information system does not, however, solve all of the supply chain and their effectiveness -related problems, because also the company’s processes and human activities have a major impact.

Characteristics of urban heat island (UHI) in a high latitude coastal city - a case study of Turku, SW Finland

The term urban heat island (UHI) refers to the common situation in which the city is warmer than its rural surroundings. In this dissertation, the local climate, and especially the UHI, of the coastal city of Turku (182,000 inh.), SW Finland, was studied in different spatial and temporal scales. The crucial aim was to sort out the urban, topographical and water body impact on temperatures at different seasons and times of the day. In addition, the impact of weather on spatiotemporal temperature differences was studied. The relative importance of environmental factors was estimated with different modelling approaches and a large number of explanatory variables with various spatial scales. The city centre is the warmest place in the Turku area. Temperature excess relative to the coldest sites, i.e. rural areas about 10 kilometers to the NE from the centre, is on average 2 °C. Occasionally, the UHI intensity can be even 10 °C. The UHI does not prevail continuously in the Turku area, but occasionally the city centre can be colder than its surroundings. Then the term urban cool island or urban cold island (UCI) is used. The UCI is most common in daytime in spring and in summer, whereas during winter the UHI prevails throughout the day. On average, the spatial temperature differences are largest in summer, whereas the single extreme values are often observed in winter. The seasonally varying sea temperature causes the shift of relatively warm areas towards the coast in autumn and inland in spring. In the long term, urban land use was concluded to be the most important factor causing spatial temperature differences in the Turku area. The impact was mainly a warming one. The impact of water bodies was emphasised in spring and autumn, when the water temperature was relatively cold and warm, respectively. The impact of topography was on average the weakest, and was seen mainly in proneness of relatively low-lying places for cold air drainage during night-time. During inversions, however, the impact of topography was emphasised, occasionally outperforming those of urban land use and water bodies.

e-Business and collaboration: A case study of pulp supply chain

This thesis studies how the case company could digitalize its supply chain and what kind of advantages this would create in the light of supply chain efficiency. The case company manufactures several pulp products that are used for paper, fabrics and packaging products by customers worldwide. The paper and pulp industry has been paying more and more attention to increasing supply chain efficiency with new operating and service models made possible by today’s information technology. The main focus of this study is on the supply chain between the case company and its key customers and the goal is to find ways to make the operations between them as efficient as possible. The study relays heavily on collaboration techniques and digitalization technologies. In addition to a theoretical framework, the study includes several empirical studies that offer real-life examples of how these theories and technologies are applied in operating environments similar to the case company. A plan with strategic and operational levels is created according to the findings of the previous sections to support the case company’s future operations. The plan is based on an RFID-supported collaboration model that aims to advance information sharing between the supply chain partners. The time for an RFID-investment is sought to be very optimal and the benefits of such system to be noteworthy, but challenging to measure in monetary terms.

Controlling and Assessment Indirect Spend – Case Study from Beverage Industry

Over the past decades, companies’ interest in controlling indirect sourcing process has increased. New indirect procurement strategies developed for the companies are needed in order to manage their indirect costs. New cost management strategies allow companies to improve their core competences. The research methodology and used in this thesis is qualitative. The theory is based on scientific publications. Empirical data given by the case organization, and was collected in the company’s own systems and in project steering meetings. The purpose of the study was to select a new electronic system for the company and give options for the company to reduce case organization’s indirect costs. The result showed that the most effective indirect cost management strategy was adopting a new electronic procurement system.

Forecasting financial weather - can we foresee market sentiment? Spectrum of stock price behavior - NYSE case study

The desire to create a statistical or mathematical model, which would allow predicting the future changes in stock prices, was born many years ago. Economists and mathematicians are trying to solve this task by applying statistical analysis and physical laws, but there are still no satisfactory results. The main reason for this is that a stock exchange is a non-stationary, unstable and complex system, which is influenced by many factors. In this thesis the New York Stock Exchange was considered as the system to be explored. A topological analysis, basic statistical tools and singular value decomposition were conducted for understanding the behavior of the market. Two methods for normalization of initial daily closure prices by Dow Jones and S&P500 were introduced and applied for further analysis. As a result, some unexpected features were identified, such as a shape of distribution of correlation matrix, a bulk of which is shifted to the right hand side with respect to zero. Also non-ergodicity of NYSE was confirmed graphically. It was shown, that singular vectors differ from each other by a constant factor. There are for certain results no clear conclusions from this work, but it creates a good basis for the further analysis of market topology.